Thanks for the info @Toan!
It looks like the reverse read for RUA230
is corrupted then. Can you get a new copy from your sequencing center?
That is correct, as far as QIIME 2 can tell all of your files are compressed and seem to have everything in order, but we don't exhaustively check that as it would make every command much slower. Instead we only peek of the first few kilobytes since usually you can detect the wrong format with only a little bit of data. Your problem probably happens at the end of the file, so demux summarize
is the first command you run that actually reads the file in its entirety.
We do have a validate
command that we're hoping we can use for these kinds of situations in the future. It should be available later this month in the 2017.10 release.
Hopefully you can get an uncorrupted copy of RUA230_S6_L001_R2_001.fastq.gz
, let me know how importing goes afterwards!